nCounter Knowledge Base: Systems

For a normal sensitivity run of 12 samples, the prep station will complete in approximately 2 hours and 40 minutes after initiation. The high sensitivity run is about 30 minutes longer.

If the power lapse is long enough that the instrument loses power, then the reagents cannot be used again, and samples will unfortunately be lost. It is strongly recommended that both instruments (Prep Station and Digital Analyzer) are connected to an Uninterrupted Power Supply.

The deck layout validation verifies that all consumables and reagents have been placed properly on the deck. This process takes about 10 minutes to complete, and the instrument touch screen should be visually checked at this time to ensure that the full run has initiated without errors.

Instructions for fixing a bent electrode can be found in the nCounter Analysis System User Manual and/or by following the on-screen prompts on the Prep Station for “Align Electrodes”. Never use force to secure a cartridge, which could cause further bending or breaking of the electrodes. If in doubt about how to proceed, contact Support at support.spatial@bruker.com to avoid damaging the instrument or its components.

The waste container should not be lined with plastic, as a liner could cause a crash due to tips building up higher than expected. The waste container can be cleaned with a 70% Ethanol solution. It is a good practice to clean the waste container each time you discard the contents.

Prep Plates stored in an incorrect orientation for a few days (e.g. during transit) will not be significantly impacted. However, the longer the plates remain in an incorrect orientation, the risk of test failure increases. It is strongly recommended that the Prep Plates be spun down briefly then stored in their proper orientation (upright) as soon as possible upon arrival. Always check for leakage before using.

Yes, the Prep Station will ask to confirm the action before aborting a run.

The cartridge can be stored for up to 1 week, protected from light and at 4°C. Ensure it is sealed with the sticker.

For a full cartridge on the standard, Medium resolution (280 FOV), the scan is about 2 hrs 30 minutes. A full cartridge on the max resolution (555 FOV) will take 5 hours.

You can pause the Digital Analyzer at any time (for example, to add another cartridge for scanning), and the scanning of other cartridges will not be affected. If pausing is attempted and does not work please allow the Digital Analyzer to complete scanning, then download the Log Files and send them to support.spatial@bruker.com for assistance in troubleshooting.

It is recommended that upon completion of scanning the cartridge is removed, wrapped in foil or placed in an opaque box and stored at 4°C. Cartridges scanned overnight can be left on the instrument until the next morning with no detectable loss in data. Cartridges can be stored at 4C for up to one week and discarded in accordance with your laboratory regulations. If rescanning is not needed, the cartridge can be left in the instrument over the weekend.

It is recommended to power cycle the instruments once a month. Instructions to power cycle are in the nCounter Analysis System user manual. Be sure that there are no samples being processed on either instrument when they are turned off.

Routine maintenance is required for optimal system performance. Lubricate the o-rings on the Prep Station every 14 days following the protocol in the user manual. If the instrument is not use for an extended period of time, please perform o-ring lubrication followed by a dry run as per instructions in the user manual. In addition, it is recommended to power cycle the instruments once a month to ensure the on-board computers are operating efficiently and have Preventive Maintenance performed annually.

The nCounter Pro, MAX, and Flex Analysis Systems (Prep Station and Digital Analyzer) can be moved independently of a Field Service Engineer for moves within the same building. For moves between buildings, a Field Service Engineer must be on-site to assist and re-install the instrument. In some cases, this assistance may be covered under an active service contract agreement. Please contact customerservice.spatial@bruker.com for more information. The nCounter SPRINT Profiler may not be moved without a Field Service Engineer, even for short distances.

The nCounter Pro Analysis System has been validated to support a 21 CFR Part 11 environment; see our summary document for additional information. The nCounter SPRINT Profiler has not been validated to this standard.

Cartridge Definition File (CDF) defines sample-specific data to associate with the data output and defines the parameters the nCounter Digital Analyzer will use during image collection and processing. You can manually input sample information on the Digital Analyzer but this could be error prone due to formatting problems as well as keyboard characters that are not recognized by the Digital Analyzer. Thus, we recommend using the CDF utility tool which is already in the memory stick that comes with your new CodeSet, in the folder entitled CDFdata, or you can access it here with along instructions to use it: https://university.nanostring.com/cdf-utility-tool-for-ncounter-digital-analyzer

No. Use of the system does not require access to external networks. The system is designed to use only local area networks (LANs) for communication. Laboratories that do not want to expose nCounter instruments to external-facing networks have the option of not networking the Digital Analyzer. Local networking of the Digital Analyzer is needed to upload CDF and RLF files via the network. Local networking of both the Prep Station and Digital Analyzer is needed to receive email notifications from the system.

No. The nCounter Pro Analysis System does not support any type of wireless communications. (WLAN and Bluetooth are not supported). Only LAN-based connectivity is supported.

Each instrument (Prep Station, Digital Analyzer) has network firewall software enabled to control incoming LAN-based network traffic. The Windows 10 IoT firewall on nCounter instruments blocks all inbound traffic except the following, which the firewall treats as exceptions:

No communication occurs between the Prep Station and Digital Analyzer when the system is run in Life Sciences mode.

Yes. Data stored on the nCounter Pro Analysis System is encrypted to the AES-256 standard. Additionally, the hard drive is encrypted to the TPM 2.0 standard. Only LAN-based connectivity is supported.

No. The nCounter Pro Analysis System does not utilize any cloud-based storage or retrieval of data. All data generated by the system is stored locally. Customers must download data directly from the system or arrange to copy files from the system’s dedicated export directory to a network folder using SSH/SFTP.

The nCounter Pro Analysis System uses a more stringent form of data security than anti-virus and anti-malware. Both systems use Windows Defender Application Control (WDAC), which allows only approved operations and programs to run. This prevents all unauthorized executables, scripts, and code from running, providing robust protection from viruses and malware and protects the system from unauthorized software or manipulation from external sources. Because this effectively represents a closed environment, standard anti-virus products and anti-virus updates are not needed.

The software architecture of the system prevents all end-users from seeing or accessing the underlying Windows operating system. The system uses a custom shell on both the Prep Station and Digital Analyzer to prevent customer end-users from accessing the Microsoft Windows 10 IoT operating system on the Digital Analyzer and Prep Station instruments. The nCounter software application that runs on the Prep Station and Digital Analyzer instruments is the graphical user interface and serve as the custom shell. When the Prep Station and Digital Analyzer instruments boot up, this custom shell prevents the user from accessing the Windows operating system. The custom shell “locks down” the operating system by altering the interactive logon procedure. For example, if a user attempts to enter CTRL+ALT+DELETE, they would discover that this keystroke combination is disabled.

Yes. The Windows firewall on Prep Station and Digital Analyzer instruments is configured to strictly limit the communication of Windows programs and services on each instrument. All Windows programs and services are blocked from communicating unless they use a port specified as an exception in the firewall (see table under Question 2).

Since the nCounter Pro Analysis System uses a custom shell and whitelisting to protect the system from unauthorized modifications, you will not be able to independently install OS patches or any third‑party applications. Users should consult Technical Support at support.spatial@bruker.com regarding OS patches for their system.

User logins are optional on systems but may be set to required depending on how it is configuration by the customer’s system administrator. System administrators may configure their system to require logins, as desired. Once a system has been configured to require logins, user logins are necessary to operate instruments, view/download data, and access administrative or maintenance functionality. Prep Station and Digital Analyzer instruments were designed such that runs can be initiated only if the operator is standing in front of the instrument. Remote instrument operation is not supported.

Yes, a network security appliance can be used in conjunction with the nCounter Pro Analysis System. The appliance would be installed between the nCounter Pro Analysis System and the existing network per the schematic shown below:

For the nCounter Pro Analysis System to operate correctly in this configuration, the appliance would need to be configured with the following ports accessible:

NOTE: To ensure full functionality, it is recommended that a DNS entry be created that maps the system name, i.e., the serial number of the digital analyzer, to the IP address of the network security appliance.

The cartridge has been specified to perform with loading volumes from 25 – 35 µL (note that this is NOT the sample input volume). Please note that the user can add water to the hybridization reaction in order to be in the appropriate range.

It is important that you depress the pipette plunger to the second stop and create an air gap behind the sample when loading your SPRINT cartridge. This facilitates consistent sample processing. These air gaps do not need to be the same size, as the instrument will correct most variation. Always pull the pipette away from the sample port before releasing the plunger, instead of releasing the plunger immediately. The microfluidic channels are a closed system, and doing so will withdraw the sample back into the tip. For more information on loading a SPRINT cartridge, refer to https://university.nanostring.com/quick-start-guide-for-loading-a-sprint-cartridge.

If your SPRINT has software version 2.0 or later, you can redefine the associated RLF with completed runs from your instrument. From the Web App, click the Download Logs option from the main menu, then choose your desired run. Click Fix RLF to upload a new RLF and virtually rescan your data. If you need to upgrade your instrument software to version 2.0 or later, please contact support.spatial@bruker.com.

Unlike the Pro, MAX, or FLEX systems, the SPRINT does the work of the Prep Station and Digital Analyzer in one. Sample processing and scanning occur in one run, and these two processes cannot be dissociated. Once a SPRINT cartridge has been processed and scanned, it cannot be used again. If your SPRINT has software version 2.0 or later, a virtual re-scan is possible if you selected an incorrect RLF file on your initial run. When the instrument is connected through a web browser, you may access the the control center web application and click the Download Data option from the main menu, then choose your desired run. Click Fix RLF to upload a new RLF and virtually rescan your data. If you need to upgrade your instrument software to version 2.0 or later, please contact support.spatial@bruker.com.

No. If precipitate appears in Reagent C, it will not have any effect on the performance of the assay and will not cause any blockages of the system.

The SPRINT is designed to keep a variety of instrument logs in case troubleshooting or other support is needed. In the case where the instrument experiences an error outside of a run, please send the instrument logs to support.spatial@bruker.com for further assistance. To download the instrument logs that are not associated with a particular run, please use the following instructions: Open the Web App, select Administration, then select Download Logs. Under Log Type, select System, uncheck the box next to Only Include Most Recent Logs, select the Updated From box and select the desired date, select Apply, then select Download.

We recommend to leave the SPRINT instrument turned on so it can run the autoprime script automatically every 2 weeks. The autoprime script runs a small amount of reagents through the lines to help prevent salt crystal build-up, which can lead to blockages. If you plan to not use the instrument for more than 4 weeks, it is best to hibernate the instrument following the instructions here: https://university.nanostring.com/ncounter-sprint-profiler-hibernation-protocol. In addition, we recommend to have Preventive Maintenance performed once a year.

Since SPRINT is a fluidic instrument, leaving it idle for an extended period of time may result in mechanical, fluidic and optical failure. Thus, if you plan to leave the SPRINT intrument idle for 4 weeks or more, we highly recommend to hibernate the instrument. The procedure could be found here (https://university.nanostring.com/ncounter-sprint-profiler-hibernation-protocol). Please note that you will need a PIN (which is only active for a few seconds) from our Support personnel to proceed here. Please email support.spatial@bruker.com with this request along with your phone number so that we can assist you.

We do not recommend moving the nCounter SPRINT instrument by yourself. All SPRINT instruments require decommission by a Service Engineer prior to the move so that the intricate optics system can be locked down to prevent movement during the relocation. Please contact our customer service team at customerservice.spatial@bruker.com who will assist you with this request.